Step 2: You are now ready to build your project. To build your project, select Project > Build Project. You can also hit the hammer icon build icon on the toolbar to build the selected project. You may see an error e.g. "make: *** no rule to make target 'all'. This is because, in our case, we didn't tell it where the makefile is, or its name. Open the project properties (right mouse on project name in the Project Explorer view and select Properties at the bottom on the context menu). On the C/C++ Build Page, on its Builder Settings tab, uncheck "Use default build command" and change the make command to make -f hello.mak since our makefile is not named the default makefile. Click here to see an illustration (displayed in a separate window). Click OK to close the Project Properties window. Your project will probably rebuild. If not you can force a build via Project > Build Project or use the hammer icon build icon. After the project build completes, the results display in the Console view and new objects, such as binaries and includes, show in the Project Explorer view. Click here to see an illustration (displayed in a separate window).
http://help.eclipse.org/indigo/index.jsp?topic=%2Forg.eclipse.cdt.doc.user%2Fgetting_started%2Fcdt_w_import.htm